I'm not a graphics artist by any means, I'm a web pogrammer. I get layered photoshop files and have to convert them into websites. What I would normally do is save each layer individually in the images folder on the server, but this is very time consuming. What I am wondering, is there an automated way in photoshop to automatically save each layer within a folder as a flattened image or something?

You could use the segment tool to split your file in areas and then save for web, you can choose to save all segments there. However i still prefer to do it manually because you get the best control ofthe images.

How could you not figure this out by yourself? I literally just spent 1 minute looking through the PS Menus and fount it...

File -> Scripts -> Export layers to files.